imb F是各个核计算受力的计算量不均衡的程度(load imbalance of force),越接近0说明分配得越合理,并行效率损失越少
vol的解释见下
vol gives the smallest volume of a DD cell relative to the average volume. This is a measure of the load density differences in your system.
It does not have to close to 1. If it is very small, it just means that your system would be very load imbalanced when you would run it without load balancing.
The can also be an exclamation mark after the volume. This means that the load balancing was limited by the minimum cell size in one or more dimensions and some cells can not be made smaller,
"A very important point refers to the methodology employed in this investigation. The authors have used a modified B3LYP DFT functional, which is a monoreferential based methods. The low spin electronic states are described by a combination of configurations and the B3LYP wave functions is not eigenfunction of S<2>. The broken symmetry approach employed in this work can palliate in some way this drawback but not systematically and, in this case, this could be critical. ?The authors do no mention which is the projection of values S<2> in any case. ?I would appreciate a comment on this point with special indication of which can of errors the use of these methods can lead."
非常感谢您。再请教一个问题,我算反应的自由能垒时加入了smd溶剂化效应,可是我并没有单独计算反应物和过渡态的溶剂化能。而是直接在高水平的单点能计算时加入了smd,然后加入低水平计算的热力学校正的thermal correction to Gibbs free energy,分别得到反应物和过渡态的溶剂效应下的自由能,然后做差。这样可以吗?以下是审稿意见:
1) it is not clear how solvent correction was computed. Difference between data in vacuo and in solvent with the small basis set? Data in solvent plus thermodynamic corrections? Please accurately describe
sob老师,请教个问题。我用gromacs时候想用oplsaa力场,所以用TPPMKTOP生成一个含100左右原子的分子的itp文件,发现电荷相加高达7.3,和中性的0相差好远,里面还有不识别的原子类型,于是我把产生的itp中原子类型和TPPMKTOP扩展库里对照,也很多找不到,或者不是想要的原子类型,有些用相近的替换了,并修改个别的电荷,有个别的在ffnonbonded.itp根据文献添加了sigma和epsilon,比如azd_n1 3.25000e-01 7.11756e-01。但是一运行还是提示不少错误。类似错误几十处,ERROR 3 [file 9_oplsaa_test.itp, line 256]:
No default Bond types ERROR 24 [file 9_oplsaa_test.itp, line 359]: No default Angle types;ERROR 130 [file 9_oplsaa_test.itp, line 756]: No default Proper Dih. types。您的培训班对这里讲的比较少,我也不知道怎么处理,请问想生成oplsaa的拓扑文件,有没有什么好的方法或者教程啊,正确的步骤是什么?谢谢您
老师,审稿意见里“The authors need to analyze the energy transition while the stacking takes place based on pi-pi bonding.”请问,这个Energy transition 是指什么,是算HOMO,LUMO电子转移那些吗?
还是刚才那个计算丙酮振动分辨电子光谱的问题。。激发态优化和频率计算完成后,在进行进行基态的优化和频率计算时,也出现了 NtrErr Called from FileIO.的报错,查看后认为是FileIO operation on non-existent file.的原因。但是Chk文件本身应该没什么问题,可以正常打开,路径和权限也没问题(在Scratch文件夹)。想问应该如何解决。谢谢了。